He said both himself, the AEC generally, and Commissioner Ed Killestyn had apologised for the lost votes, which he said prompted "a great deal of introspection" at the nation's election umpire.

Challenges from several politicians to the election outcome arising from the lost votes are currently before the High Court, while the Senate Joint Standing Committee on Electoral Matters is examining the scandal as part of its analysis of the 2013 election.

But in hearings on Thursday, the Australian National Audit Office revealed it had warned the AEC in 2010 about its vote-counting practices, but was not sure if the commission had acted on those warnings.

Auditor-General Ian McPhee said the audit office conducted audits of the commission's processes in 2002, 2004 and 2010, with the latest audit revealing problems including the opening of ballot boxes without witnesses present.

While the ANAO reviews such processes as part of its remit, it does not force government agencies to act on its recommendations; with the expectation being agencies will do so of their own accord.

But Mr Rogers told the inquiry despite the audit's evidence, and its role sitting on the AEC's business assurance committee, the ANAO had not raised such issues directly.

"I also note looking at their report that in 2007 their biggest concern was not about ballot security, it was about the (electoral) roll," he said.

"The biggest concern for the AEC is not about ballot security - it's about roll management."

However, Mr Rogers also said the lost votes were a "significant error that we are terribly embarrassed about and are now trying to address".

"We're not avoiding responsibility and accountability."

The inquiry into the 2013 federal poll continues Friday, examining the controversial flows of Senate preferences during the election.